Mail becomes unusable - Flags and Smart Mailboxes fail to load, or take an inordinate amount of time

I have had a consistent problem with my Flagged items "folder" and Smart Mailboxes in the left panel as well as any search function taking an extremely long time to sort themselves out ( > 5 minutes) where it has become faster to manually sort through thousands of emails to find what I want. I have restarted my computer, booted into safe mode (maybe a little better there?), back into normal mode, rebuilt all my inboxes/accounts, and still the same problem.

I've discussed this problem with apple support before, and it was literally a several month endeavor where I ended up having to manually re-create all of my mailbox sorting algorithms, of which I have > 100. Everything /seemed/ better, but has now devolved again to the same thing.

Is this really just a problem with local indexing? With how much time indexing (i'm assuming) seems to slow down my computer, I would hope that I would at least get some benefit from it.

Has anyone had this problem / found any tenable solutions?